Spanish populations of the white-clawed crayfish have declined sharply over the last three decades. Although Austropotamobius pallipes was once widely distributed and very abundant in most of the limestone basins of the country, outbreaks of crayfish plague since 1978 have reduced its populations, and now only some 500-600 small populations are left. 2. Consequently, the species now enjoys protection under national legislation. Management decisions regarding the conservation of a threatened species require an understanding of the genetic structure of its populations. 3. Using random amplified polymorphic DNA (RAPD) fingerprinting the genetic variability of 11 populations of A. pallipes was assessed over the species' range in Spain, and their phylogenetic relationships determined. 4. Substantial genetic differentiation was detected among the populations tested; no clear relationship was found between patterns of genetic variability and hydrological basin. The RAPD markers showed the degree of genetic variability of these populations to be similar to, and in some cases slightly higher than, that reported in previous studies on other Spanish and European populations of A. pallipes. 5. The results offer hope for the recovery of this species in Spain, and provide information that might be useful in the management of crayfish reintroduction programmes.